9ZZK | pdb_00009zzk

One Lmod2 and incoming actin at the pointed end of F-actin

PDB DOI: https://doi.org/10.2210/pdb9ZZK/pdb
EM Map EMD-75004: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Oryctolagus cuniculus, Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2026-01-07 Released: 2026-06-24
Deposition Author(s): Brotzman, S.B., Palmer, N.J., Dominguez, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.06 Å
Resolution: 4.06 Å
Resolution: 4.06 Å
Resolution: 4.06 Å
Resolution: 4.06 Å
Resolution: 4.06 Å
Resolution: 4.06 Å
Resolution: 4.06 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Lmod2 is a processive pointed-end elongator of actin filaments

Biswas, S., Brotzman, S.B., Palmer, N.J., Larrinaga, T.M., Boczkowska, M., Choubey, S., Gregorio, C.C., Dominguez, R., Shekar, S.

To be published.

Macromolecule Content

Total Structure Weight: 316.91 kDa
Atom Count: 18,791
Modeled Residue Count: 2,378
Deposited Residue Count: 2,806
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A B C D E A, B, C, D, E, G [auth O]	375	Oryctolagus cuniculus	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135 Go to UniProtKB: P68135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leiomodin-2	F [auth M]	556	Homo sapiens	Mutation(s): 0 Gene Names: LMOD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P5Q4 (Homo sapiens) Explore Q6P5Q4 Go to UniProtKB: Q6P5Q4
PHAROS: Q6P5Q4 GTEx: ENSG00000170807
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6P5Q4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain S [auth O] MOL2 format, chain S [auth O] mmCIF format, chain S [auth O]	S [auth O]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain S [auth O] Interactions & Density Focus chain S [auth O]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E]	H [auth A], J [auth B], L [auth C], N [auth D], P [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth O] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth O] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth O]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], R [auth O]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth O] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth O]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A B C D E A, B, C, D, E, G [auth O]	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.06 Å
Resolution: 4.06 Å
Resolution: 4.06 Å
Resolution: 4.06 Å
Resolution: 4.06 Å
Resolution: 4.06 Å
Resolution: 4.06 Å
Resolution: 4.06 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	PHENIX
RECONSTRUCTION	PHENIX
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Brotzman, S.B.

Palmer, N.J.

Dominguez, R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM152412
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	5R01GM073791
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	5T32AR053461-20